7A2P | pdb_00007a2p

Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant at pH 5.0 with PEG

PDB DOI: https://doi.org/10.2210/pdb7A2P/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-08-18 Released: 2021-08-25
Deposition Author(s): Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.90 Å
R-Value Free:
0.150 (Depositor), 0.139 (DCC)
R-Value Work:
0.131 (Depositor), 0.132 (DCC)
R-Value Observed:
0.132 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant at pH 5.0 with PEG

Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 7.02 kDa
Atom Count: 570
Modeled Residue Count: 59
Deposited Residue Count: 61
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Fyn	A	61	Homo sapiens	Mutation(s): 5 Gene Names: FYN EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06241 (Homo sapiens) Explore P06241 Go to UniProtKB: P06241
PHAROS: P06241 GTEx: ENSG00000010810
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06241
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.90 Å
R-Value Free: 0.150 (Depositor), 0.139 (DCC)
R-Value Work: 0.131 (Depositor), 0.132 (DCC)
R-Value Observed: 0.132 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.312	α = 90
b = 32.032	β = 90
c = 59.893	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-25

Deposition Author(s):

Camara-Artigas, A.

Plaza-Garrido, M.

Salinas-Garcia, M.C.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2016-78020-R

Revision History (Full details and data files)

Version 1.0: 2021-08-25
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.